If you could just see the water from a stationary reference frame (maybe a floating hot air balloon), you would see the water indeed falling down. Now, I remember that I said “falling down” and not “moving down”. The water actually might be moving up. The key is that even though it is moving up, it is accelerating down. The plane also is accelerating down. As long as the downward acceleration of the plane is greater than the water, the water will move into the cup above it.